It has gotten to the point where he doesn’t raise his arms at all unless required to do so. He has even figured a way to dress without lifting his arms above his shoulders.
It’s just one of those things that you do that eventually gets associated with something completely unrelated, like the way you can train a dog to obey orders by associating a command with food.
Of course, in his mind, he knows that he’s not the true cause of these many plagues; that stretching out his staff is more symbolic or a show than anything. He knows, but his body still makes the association between his now deadly arms and these horrific plagues.
He knows he’s not causing the plauges – not anymore than the dog causes its master to shout a command – but his mind isn’t made of candles, where lit ones could be put out whenever he wants.
Nevertheless, he has a job to do, so he picks up his staff, stretches sideways, and moves on.